FMO DATABASE

FMODB ID: JVQZ9

Calculation Name: 1ZBD-B-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-triphosphate

Ligand 3-letter code: GTP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ZBD

Chain ID: B

ChEMBL ID:

UniProt ID: P63012

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-903191.576445
FMO2-HF: Nuclear repulsion	850840.80768
FMO2-HF: Total energy	-52350.768765
FMO2-MP2: Total energy	-52493.86362

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:44:GLU)

Summations of interaction energy for fragment #1(A:44:GLU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
5.639	7.491	-0.002	-0.92	-0.93	-0.002

Interaction energy analysis for fragmet #1(A:44:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.147 / q_NPA : -0.079

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	46	LEU	0	-0.023	-0.008	3.582	4.747	6.599	-0.002	-0.920	-0.930	-0.002
4	A	47	THR	0	0.003	-0.005	6.111	1.339	1.339	0.000	0.000	0.000	0.000
5	A	48	ASP	-1	-0.862	-0.914	8.048	0.501	0.501	0.000	0.000	0.000	0.000
6	A	49	GLU	-1	-0.949	-0.984	11.864	1.263	1.263	0.000	0.000	0.000	0.000
7	A	50	GLU	-1	-0.873	-0.957	9.595	0.078	0.078	0.000	0.000	0.000	0.000
8	A	51	LYS	1	0.854	0.921	7.999	-5.636	-5.636	0.000	0.000	0.000	0.000
9	A	52	GLU	-1	-0.821	-0.886	11.400	1.539	1.539	0.000	0.000	0.000	0.000
10	A	53	ILE	0	-0.064	-0.023	14.701	-0.077	-0.077	0.000	0.000	0.000	0.000
11	A	54	ILE	0	0.014	0.001	9.320	-0.102	-0.102	0.000	0.000	0.000	0.000
12	A	55	ASN	0	0.021	-0.010	12.087	0.360	0.360	0.000	0.000	0.000	0.000
13	A	56	ARG	1	0.807	0.891	14.448	-1.684	-1.684	0.000	0.000	0.000	0.000
14	A	57	VAL	0	-0.089	-0.046	15.489	-0.261	-0.261	0.000	0.000	0.000	0.000
15	A	58	ILE	0	0.022	0.025	11.086	-0.227	-0.227	0.000	0.000	0.000	0.000
16	A	59	ALA	0	0.056	0.036	15.769	-0.218	-0.218	0.000	0.000	0.000	0.000
17	A	60	ARG	1	0.885	0.932	18.747	-1.702	-1.702	0.000	0.000	0.000	0.000
18	A	61	ALA	0	-0.002	0.011	17.782	-0.198	-0.198	0.000	0.000	0.000	0.000
19	A	62	GLU	-1	-0.818	-0.915	16.312	3.347	3.347	0.000	0.000	0.000	0.000
20	A	63	LYS	1	0.955	0.983	20.188	-1.461	-1.461	0.000	0.000	0.000	0.000
21	A	64	MET	0	-0.032	-0.013	22.968	-0.151	-0.151	0.000	0.000	0.000	0.000
22	A	65	GLU	-1	-0.906	-0.960	21.095	1.839	1.839	0.000	0.000	0.000	0.000
23	A	66	THR	0	-0.034	-0.029	23.551	-0.090	-0.090	0.000	0.000	0.000	0.000
24	A	67	MET	0	-0.005	-0.010	25.780	-0.119	-0.119	0.000	0.000	0.000	0.000
25	A	68	GLU	-1	-0.824	-0.875	25.955	1.012	1.012	0.000	0.000	0.000	0.000
26	A	69	GLN	0	0.028	0.002	24.635	-0.188	-0.188	0.000	0.000	0.000	0.000
27	A	70	GLU	-1	-0.966	-0.976	28.357	1.020	1.020	0.000	0.000	0.000	0.000
28	A	71	ARG	1	0.667	0.811	30.124	-1.070	-1.070	0.000	0.000	0.000	0.000
29	A	72	ILE	0	-0.017	-0.013	28.183	-0.090	-0.090	0.000	0.000	0.000	0.000
30	A	73	GLY	0	0.038	0.019	31.946	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	74	ARG	1	0.986	0.993	33.459	-0.891	-0.891	0.000	0.000	0.000	0.000
32	A	75	LEU	0	-0.078	-0.035	34.879	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	76	VAL	0	0.006	0.011	33.339	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	77	ASP	-1	-0.857	-0.929	36.712	0.834	0.834	0.000	0.000	0.000	0.000
35	A	78	ARG	1	0.798	0.887	38.979	-0.634	-0.634	0.000	0.000	0.000	0.000
36	A	79	LEU	0	0.001	0.004	38.493	-0.042	-0.042	0.000	0.000	0.000	0.000
37	A	80	GLU	-1	-0.824	-0.938	37.936	0.722	0.722	0.000	0.000	0.000	0.000
38	A	81	THR	0	-0.063	-0.034	41.633	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	82	MET	0	-0.063	-0.030	44.511	-0.027	-0.027	0.000	0.000	0.000	0.000
40	A	83	ARG	1	0.844	0.911	39.499	-0.673	-0.673	0.000	0.000	0.000	0.000
41	A	84	LYS	1	0.945	0.971	43.106	-0.660	-0.660	0.000	0.000	0.000	0.000
42	A	85	ASN	0	-0.091	-0.035	47.323	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	86	VAL	0	-0.047	-0.013	48.137	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	87	ALA	0	0.022	0.013	51.060	0.003	0.003	0.000	0.000	0.000	0.000
45	A	88	GLY	0	-0.036	-0.018	54.280	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	89	ASP	-1	-0.804	-0.913	54.026	0.336	0.336	0.000	0.000	0.000	0.000
47	A	90	GLY	0	-0.025	-0.017	53.513	0.014	0.014	0.000	0.000	0.000	0.000
48	A	91	VAL	0	-0.062	-0.009	54.568	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	92	ASN	0	0.032	0.007	57.361	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	93	ARG	1	0.863	0.930	58.396	-0.308	-0.308	0.000	0.000	0.000	0.000
51	A	94	CYS	0	-0.048	0.017	56.114	0.016	0.016	0.000	0.000	0.000	0.000
52	A	95	ILE	0	0.035	0.009	50.330	0.007	0.007	0.000	0.000	0.000	0.000
53	A	96	LEU	0	-0.022	-0.011	49.678	0.010	0.010	0.000	0.000	0.000	0.000
54	A	97	CYS	0	0.024	0.024	53.047	0.003	0.003	0.000	0.000	0.000	0.000
55	A	98	GLY	0	0.058	0.041	56.489	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	99	GLU	-1	-0.860	-0.948	58.389	0.280	0.280	0.000	0.000	0.000	0.000
57	A	100	GLN	0	0.004	-0.005	60.666	0.009	0.009	0.000	0.000	0.000	0.000
58	A	101	LEU	0	0.003	0.005	58.390	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	102	GLY	0	0.003	0.007	63.061	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	103	MET	0	-0.004	-0.022	65.838	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	104	LEU	0	-0.010	0.010	66.465	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	105	GLY	0	0.027	0.009	68.187	0.004	0.004	0.000	0.000	0.000	0.000
63	A	106	SER	0	-0.039	0.000	63.433	0.004	0.004	0.000	0.000	0.000	0.000
64	A	107	ALA	0	0.010	0.003	63.048	0.003	0.003	0.000	0.000	0.000	0.000
65	A	108	SER	0	-0.001	-0.021	58.174	0.013	0.013	0.000	0.000	0.000	0.000
66	A	109	VAL	0	-0.018	0.003	54.691	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	110	VAL	0	0.016	0.002	51.824	0.006	0.006	0.000	0.000	0.000	0.000
68	A	111	CYS	-1	-0.849	-0.730	48.083	0.420	0.420	0.000	0.000	0.000	0.000
69	A	112	GLU	-1	-0.846	-0.949	46.990	0.355	0.355	0.000	0.000	0.000	0.000
70	A	113	ASP	-1	-0.760	-0.843	42.881	0.484	0.484	0.000	0.000	0.000	0.000
71	A	114	CYS	0	-0.067	-0.113	44.393	0.013	0.013	0.000	0.000	0.000	0.000
72	A	115	LYS	1	0.820	0.908	45.824	-0.387	-0.387	0.000	0.000	0.000	0.000
73	A	116	LYS	1	0.955	0.991	47.986	-0.456	-0.456	0.000	0.000	0.000	0.000
74	A	117	ASN	0	-0.014	-0.009	51.935	0.000	0.000	0.000	0.000	0.000	0.000
75	A	118	VAL	0	0.002	-0.029	52.453	0.013	0.013	0.000	0.000	0.000	0.000
76	A	119	CYS	0	0.061	0.032	55.564	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	120	THR	0	0.041	0.006	56.839	0.014	0.014	0.000	0.000	0.000	0.000
78	A	121	LYS	1	0.910	0.956	57.046	-0.289	-0.289	0.000	0.000	0.000	0.000
79	A	122	CYS	0	-0.019	-0.025	53.841	0.013	0.013	0.000	0.000	0.000	0.000
80	A	123	GLY	0	-0.004	0.008	52.557	0.019	0.019	0.000	0.000	0.000	0.000
81	A	124	VAL	0	-0.043	-0.035	50.202	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	125	GLU	-1	-0.880	-0.931	51.445	0.262	0.262	0.000	0.000	0.000	0.000
83	A	126	THR	0	-0.089	-0.058	47.415	0.008	0.008	0.000	0.000	0.000	0.000
84	A	127	SER	0	0.039	0.006	50.323	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	128	ASN	0	-0.011	-0.007	46.650	0.003	0.003	0.000	0.000	0.000	0.000
86	A	129	ASN	0	0.002	-0.004	48.805	0.002	0.002	0.000	0.000	0.000	0.000
87	A	130	ARG	1	0.955	0.971	47.409	-0.258	-0.258	0.000	0.000	0.000	0.000
88	A	131	PRO	0	0.025	0.007	52.678	0.009	0.009	0.000	0.000	0.000	0.000
89	A	132	HIS	0	-0.035	-0.007	53.857	0.003	0.003	0.000	0.000	0.000	0.000
90	A	133	PRO	0	0.022	0.031	52.450	0.008	0.008	0.000	0.000	0.000	0.000
91	A	134	VAL	0	0.036	0.025	47.482	0.000	0.000	0.000	0.000	0.000	0.000
92	A	135	TRP	0	0.031	0.027	50.587	0.013	0.013	0.000	0.000	0.000	0.000
93	A	136	LEU	0	0.028	0.008	45.289	0.013	0.013	0.000	0.000	0.000	0.000
94	A	137	CYS	0	-0.051	-0.076	47.886	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	138	LYS	1	0.932	0.946	47.803	-0.343	-0.343	0.000	0.000	0.000	0.000
96	A	139	ILE	0	0.014	0.010	44.337	0.016	0.016	0.000	0.000	0.000	0.000
97	A	140	CYS	0	-0.016	-0.040	43.561	0.035	0.035	0.000	0.000	0.000	0.000
98	A	141	LEU	0	0.016	0.019	43.093	0.014	0.014	0.000	0.000	0.000	0.000
99	A	142	GLU	-1	-0.792	-0.879	41.254	0.608	0.608	0.000	0.000	0.000	0.000
100	A	143	GLN	0	0.011	0.020	37.046	0.031	0.031	0.000	0.000	0.000	0.000
101	A	144	ARG	1	0.843	0.886	38.323	-0.414	-0.414	0.000	0.000	0.000	0.000
102	A	145	GLU	-1	-0.846	-0.903	38.149	0.545	0.545	0.000	0.000	0.000	0.000
103	A	146	VAL	0	0.020	0.006	35.169	0.034	0.034	0.000	0.000	0.000	0.000
104	A	147	TRP	0	0.018	0.014	34.003	0.035	0.035	0.000	0.000	0.000	0.000
105	A	148	LYS	1	0.826	0.897	33.142	-0.489	-0.489	0.000	0.000	0.000	0.000
106	A	149	ARG	1	0.931	0.967	33.096	-0.615	-0.615	0.000	0.000	0.000	0.000
107	A	150	SER	0	0.029	-0.002	30.672	0.038	0.038	0.000	0.000	0.000	0.000
108	A	151	GLY	0	0.014	0.015	28.691	0.081	0.081	0.000	0.000	0.000	0.000
109	A	152	ALA	0	0.009	0.007	28.786	0.019	0.019	0.000	0.000	0.000	0.000
110	A	153	TRP	0	-0.015	-0.016	29.962	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	154	PHE	0	-0.045	0.000	23.494	-0.053	-0.053	0.000	0.000	0.000	0.000
112	A	155	PHE	0	0.000	-0.022	21.849	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	156	LYS	1	0.886	0.958	26.632	-0.838	-0.838	0.000	0.000	0.000	0.000
114	A	157	GLY	0	0.024	0.017	28.661	-0.024	-0.024	0.000	0.000	0.000	0.000
115	A	158	PHE	0	0.006	-0.005	26.983	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	159	PRO	0	-0.003	0.012	21.383	0.063	0.063	0.000	0.000	0.000	0.000
117	A	160	LYS	1	0.966	0.963	20.703	-1.938	-1.938	0.000	0.000	0.000	0.000
118	A	161	GLN	0	0.013	0.012	17.189	0.318	0.318	0.000	0.000	0.000	0.000
119	A	162	VAL	0	-0.004	-0.003	14.874	-0.039	-0.039	0.000	0.000	0.000	0.000
120	A	163	LEU	0	-0.017	-0.006	10.812	0.560	0.560	0.000	0.000	0.000	0.000
121	A	164	PRO	0	0.023	0.017	11.271	-0.316	-0.316	0.000	0.000	0.000	0.000
122	A	165	GLN	0	-0.034	-0.035	10.878	0.859	0.859	0.000	0.000	0.000	0.000
123	A	166	PRO	0	-0.027	0.004	7.459	-0.067	-0.067	0.000	0.000	0.000	0.000
124	A	167	MET	-1	-0.818	-0.886	9.552	4.834	4.834	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:44:GLU)